Per chromosome imputation report for cohort WTCCC.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 25.6.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 17693496 | 79.371 |
| 0.1 | 1220691 | 5.476 |
| 0.2 | 811049 | 3.638 |
| 0.3 | 617468 | 2.770 |
| 0.4 | 495367 | 2.222 |
| 0.5 | 405424 | 1.819 |
| 0.6 | 348644 | 1.564 |
| 0.7 | 290764 | 1.304 |
| 0.8 | 241135 | 1.082 |
| 0.9 | 167965 | 0.753 |
| Total | 22292003 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 1333464 | 5.982 |
| 0.4 | 1594714 | 7.154 |
| 0.5 | 2087218 | 9.363 |
| 0.6 | 2712129 | 12.166 |
| 0.7 | 3226998 | 14.476 |
| 0.8 | 3486713 | 15.641 |
| 0.9 | 7803643 | 35.006 |
| 1.0 | 47124 | 0.211 |
| Total | 22292003 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1345942 | 79.7599 |
| 0.1 | 89397 | 5.2976 |
| 0.2 | 57934 | 3.4331 |
| 0.3 | 45304 | 2.6847 |
| 0.4 | 37430 | 2.2181 |
| 0.5 | 30395 | 1.8012 |
| 0.6 | 27133 | 1.6079 |
| 0.7 | 21666 | 1.2839 |
| 0.8 | 18623 | 1.1036 |
| 0.9 | 13668 | 0.8100 |
| Total | 1687492 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 102306 | 6.0626 |
| 0.4 | 123216 | 7.3017 |
| 0.5 | 159741 | 9.4662 |
| 0.6 | 207463 | 12.2942 |
| 0.7 | 248457 | 14.7234 |
| 0.8 | 265194 | 15.7153 |
| 0.9 | 577626 | 34.2299 |
| 1.0 | 3489 | 0.2068 |
| Total | 1687492 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1506704 | 80.1031 |
| 0.1 | 100488 | 5.3424 |
| 0.2 | 66180 | 3.5184 |
| 0.3 | 49415 | 2.6271 |
| 0.4 | 38604 | 2.0524 |
| 0.5 | 32741 | 1.7407 |
| 0.6 | 28717 | 1.5267 |
| 0.7 | 23366 | 1.2422 |
| 0.8 | 20128 | 1.0701 |
| 0.9 | 14612 | 0.7768 |
| Total | 1880955 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 104290 | 5.5445 |
| 0.4 | 125973 | 6.6973 |
| 0.5 | 167537 | 8.9070 |
| 0.6 | 225763 | 12.0026 |
| 0.7 | 277451 | 14.7505 |
| 0.8 | 298195 | 15.8534 |
| 0.9 | 678170 | 36.0546 |
| 1.0 | 3576 | 0.1901 |
| Total | 1880955 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1270224 | 79.7069 |
| 0.1 | 87647 | 5.4999 |
| 0.2 | 55292 | 3.4696 |
| 0.3 | 43158 | 2.7082 |
| 0.4 | 34889 | 2.1893 |
| 0.5 | 29248 | 1.8353 |
| 0.6 | 24676 | 1.5484 |
| 0.7 | 20503 | 1.2866 |
| 0.8 | 16581 | 1.0405 |
| 0.9 | 11400 | 0.7154 |
| Total | 1593618 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 87243 | 5.4745 |
| 0.4 | 103639 | 6.5034 |
| 0.5 | 140596 | 8.8224 |
| 0.6 | 189808 | 11.9105 |
| 0.7 | 233026 | 14.6225 |
| 0.8 | 254232 | 15.9531 |
| 0.9 | 581652 | 36.4988 |
| 1.0 | 3422 | 0.2147 |
| Total | 1593618 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1227049 | 78.8301 |
| 0.1 | 82075 | 5.2728 |
| 0.2 | 60584 | 3.8921 |
| 0.3 | 44897 | 2.8843 |
| 0.4 | 34125 | 2.1923 |
| 0.5 | 27812 | 1.7867 |
| 0.6 | 24485 | 1.5730 |
| 0.7 | 21599 | 1.3876 |
| 0.8 | 19853 | 1.2754 |
| 0.9 | 14095 | 0.9055 |
| Total | 1556574 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 86606 | 5.5639 |
| 0.4 | 103230 | 6.6319 |
| 0.5 | 138191 | 8.8779 |
| 0.6 | 183713 | 11.8024 |
| 0.7 | 223539 | 14.3610 |
| 0.8 | 246091 | 15.8098 |
| 0.9 | 572213 | 36.7611 |
| 1.0 | 2991 | 0.1922 |
| Total | 1556574 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1151415 | 79.7524 |
| 0.1 | 76873 | 5.3246 |
| 0.2 | 53070 | 3.6759 |
| 0.3 | 40305 | 2.7917 |
| 0.4 | 31692 | 2.1951 |
| 0.5 | 24633 | 1.7062 |
| 0.6 | 22387 | 1.5506 |
| 0.7 | 18246 | 1.2638 |
| 0.8 | 14978 | 1.0374 |
| 0.9 | 10138 | 0.7022 |
| Total | 1443737 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 79499 | 5.5065 |
| 0.4 | 93612 | 6.4840 |
| 0.5 | 124811 | 8.6450 |
| 0.6 | 167946 | 11.6327 |
| 0.7 | 208542 | 14.4446 |
| 0.8 | 230392 | 15.9580 |
| 0.9 | 535342 | 37.0803 |
| 1.0 | 3593 | 0.2489 |
| Total | 1443737 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1103480 | 78.7379 |
| 0.1 | 81694 | 5.8292 |
| 0.2 | 52876 | 3.7729 |
| 0.3 | 40125 | 2.8631 |
| 0.4 | 32829 | 2.3425 |
| 0.5 | 25766 | 1.8385 |
| 0.6 | 22641 | 1.6155 |
| 0.7 | 17131 | 1.2224 |
| 0.8 | 15158 | 1.0816 |
| 0.9 | 9759 | 0.6963 |
| Total | 1401459 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 70614 | 5.0386 |
| 0.4 | 83074 | 5.9277 |
| 0.5 | 113610 | 8.1066 |
| 0.6 | 155185 | 11.0731 |
| 0.7 | 195753 | 13.9678 |
| 0.8 | 220607 | 15.7412 |
| 0.9 | 559043 | 39.8901 |
| 1.0 | 3573 | 0.2549 |
| Total | 1401459 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 993650 | 79.1716 |
| 0.1 | 69631 | 5.5480 |
| 0.2 | 47598 | 3.7925 |
| 0.3 | 35554 | 2.8329 |
| 0.4 | 28546 | 2.2745 |
| 0.5 | 23636 | 1.8833 |
| 0.6 | 18863 | 1.5030 |
| 0.7 | 16324 | 1.3007 |
| 0.8 | 12185 | 0.9709 |
| 0.9 | 9071 | 0.7228 |
| Total | 1255058 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 74813 | 5.9609 |
| 0.4 | 88562 | 7.0564 |
| 0.5 | 116656 | 9.2949 |
| 0.6 | 151989 | 12.1101 |
| 0.7 | 182312 | 14.5262 |
| 0.8 | 197684 | 15.7510 |
| 0.9 | 440874 | 35.1278 |
| 1.0 | 2168 | 0.1727 |
| Total | 1255058 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 982076 | 79.9015 |
| 0.1 | 64043 | 5.2105 |
| 0.2 | 44346 | 3.6080 |
| 0.3 | 32585 | 2.6511 |
| 0.4 | 27647 | 2.2494 |
| 0.5 | 21353 | 1.7373 |
| 0.6 | 19384 | 1.5771 |
| 0.7 | 15567 | 1.2665 |
| 0.8 | 13088 | 1.0648 |
| 0.9 | 9020 | 0.7339 |
| Total | 1229109 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 70169 | 5.7089 |
| 0.4 | 82312 | 6.6969 |
| 0.5 | 106170 | 8.6380 |
| 0.6 | 143133 | 11.6453 |
| 0.7 | 179179 | 14.5780 |
| 0.8 | 193940 | 15.7789 |
| 0.9 | 451553 | 36.7382 |
| 1.0 | 2653 | 0.2158 |
| Total | 1229109 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 746006 | 79.5217 |
| 0.1 | 53687 | 5.7229 |
| 0.2 | 34085 | 3.6333 |
| 0.3 | 24747 | 2.6379 |
| 0.4 | 20425 | 2.1772 |
| 0.5 | 15681 | 1.6715 |
| 0.6 | 14752 | 1.5725 |
| 0.7 | 11647 | 1.2415 |
| 0.8 | 9687 | 1.0326 |
| 0.9 | 7399 | 0.7887 |
| Total | 938116 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 51213 | 5.4591 |
| 0.4 | 61149 | 6.5183 |
| 0.5 | 82777 | 8.8237 |
| 0.6 | 112421 | 11.9837 |
| 0.7 | 137782 | 14.6871 |
| 0.8 | 152444 | 16.2500 |
| 0.9 | 338407 | 36.0730 |
| 1.0 | 1923 | 0.2050 |
| Total | 938116 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 869360 | 79.2817 |
| 0.1 | 60961 | 5.5594 |
| 0.2 | 39600 | 3.6113 |
| 0.3 | 28733 | 2.6203 |
| 0.4 | 24606 | 2.2440 |
| 0.5 | 20999 | 1.9150 |
| 0.6 | 16831 | 1.5349 |
| 0.7 | 14278 | 1.3021 |
| 0.8 | 12580 | 1.1472 |
| 0.9 | 8598 | 0.7841 |
| Total | 1096546 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 57844 | 5.2751 |
| 0.4 | 68408 | 6.2385 |
| 0.5 | 92033 | 8.3930 |
| 0.6 | 124598 | 11.3628 |
| 0.7 | 155836 | 14.2115 |
| 0.8 | 174303 | 15.8956 |
| 0.9 | 420520 | 38.3495 |
| 1.0 | 3004 | 0.2740 |
| Total | 1096546 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 856508 | 79.1912 |
| 0.1 | 59161 | 5.4699 |
| 0.2 | 36185 | 3.3456 |
| 0.3 | 30727 | 2.8410 |
| 0.4 | 24374 | 2.2536 |
| 0.5 | 20734 | 1.9170 |
| 0.6 | 17922 | 1.6570 |
| 0.7 | 14347 | 1.3265 |
| 0.8 | 12196 | 1.1276 |
| 0.9 | 9415 | 0.8705 |
| Total | 1081569 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 59451 | 5.4967 |
| 0.4 | 71362 | 6.5980 |
| 0.5 | 96060 | 8.8815 |
| 0.6 | 128347 | 11.8667 |
| 0.7 | 155761 | 14.4014 |
| 0.8 | 168231 | 15.5543 |
| 0.9 | 398560 | 36.8502 |
| 1.0 | 3797 | 0.3511 |
| Total | 1081569 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 829923 | 79.4763 |
| 0.1 | 56898 | 5.4488 |
| 0.2 | 35490 | 3.3986 |
| 0.3 | 30838 | 2.9532 |
| 0.4 | 22709 | 2.1747 |
| 0.5 | 18863 | 1.8064 |
| 0.6 | 16296 | 1.5606 |
| 0.7 | 12508 | 1.1978 |
| 0.8 | 12455 | 1.1927 |
| 0.9 | 8259 | 0.7909 |
| Total | 1044239 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 58803 | 5.6312 |
| 0.4 | 70280 | 6.7303 |
| 0.5 | 91267 | 8.7400 |
| 0.6 | 122922 | 11.7714 |
| 0.7 | 149002 | 14.2690 |
| 0.8 | 164334 | 15.7372 |
| 0.9 | 384979 | 36.8669 |
| 1.0 | 2652 | 0.2540 |
| Total | 1044239 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 617410 | 78.5403 |
| 0.1 | 42914 | 5.4591 |
| 0.2 | 27983 | 3.5597 |
| 0.3 | 22836 | 2.9050 |
| 0.4 | 17593 | 2.2380 |
| 0.5 | 15491 | 1.9706 |
| 0.6 | 12571 | 1.5991 |
| 0.7 | 11390 | 1.4489 |
| 0.8 | 9713 | 1.2356 |
| 0.9 | 8205 | 1.0438 |
| Total | 786106 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 40509 | 5.1531 |
| 0.4 | 48913 | 6.2222 |
| 0.5 | 67236 | 8.5530 |
| 0.6 | 92301 | 11.7415 |
| 0.7 | 115339 | 14.6722 |
| 0.8 | 127546 | 16.2250 |
| 0.9 | 292089 | 37.1564 |
| 1.0 | 2173 | 0.2764 |
| Total | 786106 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 549321 | 79.2703 |
| 0.1 | 38932 | 5.6181 |
| 0.2 | 26290 | 3.7938 |
| 0.3 | 18087 | 2.6101 |
| 0.4 | 15524 | 2.2402 |
| 0.5 | 11868 | 1.7126 |
| 0.6 | 10101 | 1.4576 |
| 0.7 | 9077 | 1.3099 |
| 0.8 | 7752 | 1.1187 |
| 0.9 | 6020 | 0.8687 |
| Total | 692972 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 40345 | 5.8220 |
| 0.4 | 49231 | 7.1043 |
| 0.5 | 64482 | 9.3051 |
| 0.6 | 84661 | 12.2171 |
| 0.7 | 100061 | 14.4394 |
| 0.8 | 107419 | 15.5012 |
| 0.9 | 245405 | 35.4134 |
| 1.0 | 1368 | 0.1974 |
| Total | 692972 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 492518 | 79.4604 |
| 0.1 | 33386 | 5.3863 |
| 0.2 | 22342 | 3.6045 |
| 0.3 | 16725 | 2.6983 |
| 0.4 | 14286 | 2.3048 |
| 0.5 | 11783 | 1.9010 |
| 0.6 | 8922 | 1.4394 |
| 0.7 | 7909 | 1.2760 |
| 0.8 | 6586 | 1.0626 |
| 0.9 | 5371 | 0.8665 |
| Total | 619828 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 38644 | 6.2346 |
| 0.4 | 47577 | 7.6758 |
| 0.5 | 61860 | 9.9802 |
| 0.6 | 78193 | 12.6153 |
| 0.7 | 91166 | 14.7083 |
| 0.8 | 96437 | 15.5587 |
| 0.9 | 204698 | 33.0250 |
| 1.0 | 1253 | 0.2022 |
| Total | 619828 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 526006 | 79.3973 |
| 0.1 | 37760 | 5.6996 |
| 0.2 | 22868 | 3.4518 |
| 0.3 | 19158 | 2.8918 |
| 0.4 | 13968 | 2.1084 |
| 0.5 | 12143 | 1.8329 |
| 0.6 | 10691 | 1.6137 |
| 0.7 | 9507 | 1.4350 |
| 0.8 | 6350 | 0.9585 |
| 0.9 | 4048 | 0.6110 |
| Total | 662499 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 45638 | 6.8888 |
| 0.4 | 54667 | 8.2516 |
| 0.5 | 69965 | 10.5608 |
| 0.6 | 86308 | 13.0276 |
| 0.7 | 98309 | 14.8391 |
| 0.8 | 105731 | 15.9594 |
| 0.9 | 201179 | 30.3667 |
| 1.0 | 702 | 0.1060 |
| Total | 662499 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 447828 | 79.1034 |
| 0.1 | 30175 | 5.3300 |
| 0.2 | 23007 | 4.0639 |
| 0.3 | 15474 | 2.7333 |
| 0.4 | 13553 | 2.3940 |
| 0.5 | 11126 | 1.9653 |
| 0.6 | 8804 | 1.5551 |
| 0.7 | 7903 | 1.3960 |
| 0.8 | 5663 | 1.0003 |
| 0.9 | 2597 | 0.4587 |
| Total | 566130 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 49426 | 8.7305 |
| 0.4 | 58937 | 10.4105 |
| 0.5 | 72219 | 12.7566 |
| 0.6 | 80783 | 14.2693 |
| 0.7 | 82831 | 14.6311 |
| 0.8 | 83333 | 14.7198 |
| 0.9 | 138073 | 24.3889 |
| 1.0 | 528 | 0.0933 |
| Total | 566130 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 484441 | 78.9282 |
| 0.1 | 33988 | 5.5375 |
| 0.2 | 23447 | 3.8201 |
| 0.3 | 17670 | 2.8789 |
| 0.4 | 13935 | 2.2704 |
| 0.5 | 11035 | 1.7979 |
| 0.6 | 9453 | 1.5401 |
| 0.7 | 8068 | 1.3145 |
| 0.8 | 6555 | 1.0680 |
| 0.9 | 5182 | 0.8443 |
| Total | 613774 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 35898 | 5.8487 |
| 0.4 | 44056 | 7.1779 |
| 0.5 | 60214 | 9.8105 |
| 0.6 | 77949 | 12.7000 |
| 0.7 | 90889 | 14.8082 |
| 0.8 | 96319 | 15.6929 |
| 0.9 | 207261 | 33.7683 |
| 1.0 | 1188 | 0.1936 |
| Total | 613774 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 328366 | 77.4331 |
| 0.1 | 28336 | 6.6820 |
| 0.2 | 18721 | 4.4147 |
| 0.3 | 12930 | 3.0491 |
| 0.4 | 9591 | 2.2617 |
| 0.5 | 8155 | 1.9231 |
| 0.6 | 6711 | 1.5825 |
| 0.7 | 5748 | 1.3555 |
| 0.8 | 3915 | 0.9232 |
| 0.9 | 1591 | 0.3752 |
| Total | 424064 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 47353 | 11.1665 |
| 0.4 | 54546 | 12.8627 |
| 0.5 | 60140 | 14.1818 |
| 0.6 | 60491 | 14.2646 |
| 0.7 | 56548 | 13.3348 |
| 0.8 | 57040 | 13.4508 |
| 0.9 | 87544 | 20.6441 |
| 1.0 | 402 | 0.0948 |
| Total | 424064 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 386835 | 79.4252 |
| 0.1 | 27298 | 5.6048 |
| 0.2 | 18103 | 3.7169 |
| 0.3 | 13424 | 2.7562 |
| 0.4 | 11186 | 2.2967 |
| 0.5 | 8898 | 1.8269 |
| 0.6 | 7669 | 1.5746 |
| 0.7 | 5944 | 1.2204 |
| 0.8 | 4671 | 0.9591 |
| 0.9 | 3015 | 0.6190 |
| Total | 487043 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 31294 | 6.4253 |
| 0.4 | 38617 | 7.9289 |
| 0.5 | 51012 | 10.4738 |
| 0.6 | 64486 | 13.2403 |
| 0.7 | 70903 | 14.5579 |
| 0.8 | 73882 | 15.1695 |
| 0.9 | 156030 | 32.0362 |
| 1.0 | 819 | 0.1682 |
| Total | 487043 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 223930 | 78.0056 |
| 0.1 | 15688 | 5.4649 |
| 0.2 | 10134 | 3.5302 |
| 0.3 | 9074 | 3.1609 |
| 0.4 | 7180 | 2.5011 |
| 0.5 | 5975 | 2.0814 |
| 0.6 | 4872 | 1.6972 |
| 0.7 | 4491 | 1.5644 |
| 0.8 | 3998 | 1.3927 |
| 0.9 | 1727 | 0.6016 |
| Total | 287069 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 19245 | 6.7040 |
| 0.4 | 23038 | 8.0252 |
| 0.5 | 30822 | 10.7368 |
| 0.6 | 38490 | 13.4079 |
| 0.7 | 41785 | 14.5557 |
| 0.8 | 42346 | 14.7512 |
| 0.9 | 90688 | 31.5910 |
| 1.0 | 655 | 0.2282 |
| Total | 287069 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 217559 | 78.4627 |
| 0.1 | 15874 | 5.7250 |
| 0.2 | 11143 | 4.0187 |
| 0.3 | 7964 | 2.8722 |
| 0.4 | 6903 | 2.4896 |
| 0.5 | 5243 | 1.8909 |
| 0.6 | 4693 | 1.6925 |
| 0.7 | 3898 | 1.4058 |
| 0.8 | 2598 | 0.9370 |
| 0.9 | 1402 | 0.5056 |
| Total | 277277 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 22961 | 8.2809 |
| 0.4 | 27154 | 9.7931 |
| 0.5 | 33062 | 11.9238 |
| 0.6 | 39327 | 14.1833 |
| 0.7 | 39590 | 14.2781 |
| 0.8 | 39770 | 14.3431 |
| 0.9 | 75123 | 27.0931 |
| 1.0 | 290 | 0.1046 |
| Total | 277277 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 536945 | 80.5294 |
| 0.1 | 33785 | 5.0670 |
| 0.2 | 23771 | 3.5651 |
| 0.3 | 17738 | 2.6603 |
| 0.4 | 13772 | 2.0655 |
| 0.5 | 11846 | 1.7766 |
| 0.6 | 10070 | 1.5103 |
| 0.7 | 9647 | 1.4468 |
| 0.8 | 5822 | 0.8732 |
| 0.9 | 3373 | 0.5059 |
| Total | 666769 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 59300 | 8.8936 |
| 0.4 | 73161 | 10.9725 |
| 0.5 | 86757 | 13.0116 |
| 0.6 | 95852 | 14.3756 |
| 0.7 | 92937 | 13.9384 |
| 0.8 | 91243 | 13.6843 |
| 0.9 | 166614 | 24.9883 |
| 1.0 | 905 | 0.1357 |
| Total | 666769 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering